Effects on Translation Pausing of Alterations in Protein and RNA Components of the Ribosome Exit Tunnel
- 1 September 2008
- journal article
- Published by American Society for Microbiology in Journal of Bacteriology
- Vol. 190 (17) , 5862-5869
- https://doi.org/10.1128/jb.00632-08
Abstract
Amino acids are polymerized into peptides in the peptidyl transferase center of the ribosome. The nascent peptides then pass through the exit tunnel before they reach the extraribosomal environment. A number of nascent peptides interact with the exit tunnel and stall elongation at specific sites within their peptide chain. Several mutational changes in RNA and protein components of the ribosome have previously been shown to interfere with pausing. These changes are localized in the narrowest region of the tunnel, near a constriction formed by ribosomal proteins L4 and L22. To expand our knowledge about peptide-induced pausing, we performed a comparative study of pausing induced by two peptides, SecM and a short peptide, Crb CmlA , that requires chloramphenicol as a coinducer of pausing. We analyzed the effects of 15 mutational changes in L4 and L22, as well as the effects of methylating nucleotide A2058 of 23S rRNA, a nucleotide previously implicated in pausing and located close to the L4-L22 constriction. Our results show that methylation of A2058 and most mutational changes in L4 and L22 have differential effects on pausing in response to Crb CmlA and SecM. Only one change, a 6-amino-acid insertion after amino acid 72 in L4, affects pausing in both peptides. We conclude that the two peptides interact with different regions of the exit tunnel. Our results suggest that either the two peptides use different mechanisms of pausing or they interact differently but induce similar inhibitory conformational changes in functionally important regions of the ribosome.Keywords
This publication has 45 references indexed in Scilit:
- Novel mutations in ribosomal proteins L4 and L22 that confer erythromycin resistance in Escherichia coliMolecular Microbiology, 2007
- Translation Arrest Requires Two-Way Communication between a Nascent Polypeptide and the RibosomeMolecular Cell, 2006
- The Geometry of the Ribosomal Polypeptide Exit TunnelJournal of Molecular Biology, 2006
- Nascent peptide in the ‘birth canal’ of the ribosomeTrends in Biochemical Sciences, 2006
- Features of Ribosome-Peptidyl-tRNA Interactions Essential for Tryptophan Induction of tna Operon ExpressionMolecular Cell, 2005
- Ribosome Stalling during Translation Elongation Induces Cleavage of mRNA Being Translated in Escherichia coliPublished by Elsevier ,2004
- The extended loops of ribosomal proteins L4 and L22 are not required for ribosome assembly or L4-mediated autogenous controlRNA, 2003
- Measuring β-Galactosidase Activity in Bacteria: Cell Growth, Permeabilization, and Enzyme Assays in 96-Well ArraysBiochemical and Biophysical Research Communications, 2002
- The Complete Atomic Structure of the Large Ribosomal Subunit at 2.4 Å ResolutionScience, 2000
- A reversible change in the ability of Escherichia coli ribosomes to bind to erythromycinJournal of Molecular Biology, 1970